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Wednesday, February 4, 2015

New phytools version (phytools 0.4-45) submitted to CRAN

This afternoon I submitted a new version of phytools to
CRAN.
Assuming it is accepted, the new version (phytools 0.4-45), which is
already available from the phytools
page, should percolate through all of the CRAN mirror repositories
over the next few days.

This version does not feature any significant updates over the most recent
non-CRAN phytools release
(although I did do some updating of the manual pages this morning before
submitting); however the last CRAN update was August 26th of last year
(phytools 0.4-31) so there are many changes and updates to phytools since
that release.

Some updates and additions include the following (and I can't guarantee
that this list is comprehensive):

(1) A faster version of the robust Newick tree reader read.newick
(1,
2).

(5) Replacement of the redundant phytools function repPhylo with a
valid
alias.

(6) A
fix
for a very mysterious bug in plot.contMap and plot.densityMap
(not by coincidence - these two functions use the same internals).

(7) A wrapper function implementating
Pagel's
(1994) method to test for correlated evolution of two binary traits. (Not in
phytools, but I posted code for simulating binary character correlated evolution
here.)

About this blog

This web-log chronicles the development of new tools for phylogenetic analyses in the phytools R package. Unless you a reading a very recent page of the blog, I recommend that you install the latest CRAN version of phytools (or latest beta release) before attempting to replicate any of the analyses of this site. That is because the linked functions may be archived, and very likely have been replaced by newer versions.